[Bioperl-l] version of ExtUtils::Manifest too strict?

Chris Fields cjfields at illinois.edu
Mon Nov 9 19:50:00 EST 2009

On Nov 9, 2009, at 5:44 PM, Alex Lancaster wrote:

>>>>>> Chris Fields  writes:
>> Alex, Not sure why ExtUtils::Manifest can't be bundled as a separate
>> perl package alone.  It is part of perl core but it's also available
>> on CPAN separately from perl itself:
>> http://search.cpan.org/~rkobes/ExtUtils-Manifest-1.57/lib/ExtUtils/Manifest.pm
> Hi Chris,
> Yes, in principle it would be possible to have this split out as a
> separate package (currently it's a "subpackage" under the main perl
> package), unfortunately that's just not the way it's currently done in
> Fedora (probably because it's part of the core set and they like to
> update all relevant packages in one step) and I have little control  
> over
> that.
> As I suspected, the perl maintainer is not at all enthusiastic for
> updating the whole of perl just for that package (except for rawhide
> which would mean that bioperl 1.6.1 would not be available until F-13,
> about 6 months from now).  See:
> http://bugzilla.redhat.com/show_bug.cgi?id=533562#c1
> Obviously I am not happy with this situation either, because it will
> freeze bioperl on Fedora at 1.6.0 for about 6 months, so can you
> recommend any temporary workarounds in the meantime?

Well, if you don't absolutely require the MANIFEST for the final  
package you can forego the requirement.  The file in question that  
triggered the requirement is a data file used only for testing:

t/data/test 2.txt

>> This is the commit message for that BTW.  This allows spaces in file
>> names for the MANIFEST.  v1.52 is a bug fix and is required.
>> http://code.open-bio.org/svnweb/index.cgi/bioperl/revision/?rev=15673
> Perhaps I could create a patch that renamed files with spaces in  
> them to
> ones with no spaces and then rename them again upon installation.
> Can you point me to which files are the problematic ones that  
> triggered
> the dependency for 1.52?  Perhaps I can figure a workaround.
> Meanwhile I will press the maintainer of perl in Fedora to perhaps
> reconsider his position (e.g. if another update for perl is going out
> for another reason, like a security update, perhaps he could roll in  
> the
> 1.52 update at the same time).
> Cheers,
> Alex

I would point out that this is a fairly significant bug fix for  
ExtUtils::Manifest.  A newer point release of perl is now available  
(5.10.1) that contains the fix and has a fix for a performance  
regression that popped up in 5.10.0.


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